Pharmacogenomics of Chemotherapeutic Toxicities

Abstract

The Dolan lab is focused on improving the quality of life of cancer patients through the identification of genetic variants associated with risk for severe and persistent toxicities following chemotherapy (i.e. peripheral neuropathy, ototoxicity). To this end, they are involved in clinical genome wide association studies and developing preclinical models to elucidate the biochemical and cellular impact of genes associated with chemotherapeutic toxicity. There is a serious need for a relevant and genetically diverse human cellular model for mechanistic studies of CIPN and the development of effective neuroprotectants. Thus, induced-pluripotent stem cell derived neurons are being developed as a cellular model system to study neuropathic damage. ​

Overview

​Preclinical model of CIPN

Specific Aims

Aim 1: To uncover cellular mechanisms of chemotherapy-induced cytotoxicity by employing integrative data approaches in cell lines derived from different populations.To this end, we will utilize International HapMap cell lines, which provide samples of diverse, well-characterized ancestry, to evaluate chemotherapy-induced cytotoxicity and apoptosis. We will provide important mechanistic insights by integrating multiple large datasets including genetic variation, gene expression, miRNA, modified cytosine, and transcription factor levels, along with experimental models and techniques to characterize chemotherapeutic pharmacologic traits within the cell lines. To elucidate cellular mechanisms, the laboratory will evaluate if pharmacologic SNPs, identified through clinical GWAS, are associated with gene expression, miRNA expression or modified cytosines or protein expression.

Aim 2: To identify and functionally validate genetic variants/genes associated with chemotherapeutic induced toxicities including peripheral neuropathy and ototoxicity.Persistent chemotherapeutic induced peripheral neuropathy (CIPN) will be measured in cancer survivors after treatment with cisplatin, paclitaxel or vincristine to identify genetic variants associated with this common and devastating side effect. Moving beyond single nucleotide variants, gene- and network-based approaches aggregating SNP-level information will be employed to better understand the function of signals. Genes identified will be validated through studying the resultant effects of gene knockdown and stimulation/inhibition of pathways on cellular sensitivity to drug in human induced pluripotent stem cell (iPSC) derived neurons.

Aim 3: To establish a resource of human iPSC derived neurons from well-phenotyped cancer survivors following treatment with paclitaxel, vincristine or cisplatin to be used to identify an in vitro toxicity readout that parallels the clinical phenotype.​Human iPSC derived neurons will be generated by reprogramming peripheral blood mononuclear cells from patients who developed severe, persistent neuropathy and matched controls who did not develop neuropathy following treatment with either paclitaxel, vincristine or cisplatin. This resource will be extremely valuable in identifying genome variants that predispose to paclitaxel- vincristine- or cisplatin-induced neuropathy, and as a platform to identify drugs that can be used to mitigate this common toxicity. We will determine if there are cellular differences in neurons created from chemotherapy-sensitive patients and matched controls in their sensitivity to chemotherapeutics and determine if the differences are specific to a particular neuronal subtype.